Senior public servant Michael Pezzullo will become head of the Australian Customs and Border Protection Service (ACBPS), with a brief to stamp out corrupt conduct.

He joined the Department of Defence as a graduate in 1987 and has been ACBPS acting chief executive since September.

Home Affairs Minister Jason Clare said Mr Pezzullo has signed an order making it mandatory requirement for all Customs and Border Protection workers to report any suspected serious misconduct, corruption or criminal conduct.

Drug and alcohol testing will begin next month.

"Customs requires major structural and cultural reform and Mr Pezzullo will drive this reform program," Mr Clare said in a statement on Friday.